The Chrysalids is a novel filled with conflicts and resolutions. Three conflicts that occur in the beginning, middle and end of the book are respectively; Person vs. Self when Sophie is debating whether it is worth it to let David know her deviation, Person vs. Society when the shape-thinkers are found out and must fight against society's rules to remain alive, and a very large Person vs. Person conflict in which the Fringe people battle the Waknuk people with grave consequences.

The first conflict that we will talk about is a Person vs. Self conflict in which Sophie must battle with her conscience on whether or not to tell David about her deviation of 6 toes. Sophie is hurt and must remove her shoe to stop the swelling but in that case she would have to let someone know that she is a Blasphemy, something she has so carefully hidden all her life. In letting David in on her secret, she gains a friend and David learns that people who are different are not really disgusting and evil, something he has been brought up to believe.

The second conflict is a Person vs. Society. The shape-thinkers are found out and two have been captured. The community of Waknuk realizes that people have been living with a Deviation in their community all their lives and are frightened because they could not control these people. David, Rosalind, Petra, Michael and the others must fight against these prejudice ideas-some must run away while others must live a false existance, pretending to be someone they are not.

The third conflict is a Person vs. Person conflict when the Fringe people battle those from Waknuk. The people from Waknuk are trying to overtake the Fringe people who continue to invade their "perfect" community. The Waknuk people are also aware that the Fringe people are hiding David, Rosalind, and Petra who are on the communitiy's "Most Wanted List". The Fringe people are trying to protect themselves and fight against those who have exiled them. In a variety of locations the two parties clash resulting many Fringe casulties. While the Waknuk people and Fringe people are fighting, the Sealand people come to rescue the shape-thinkers. The Sealanders send down special plastic threads that kill everyone. The consequences of this battle are that "supernatural" forces may arrive to save the worthy ones (in this case the shape-thinkers) and destroy those who are not.